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MITgcm, 36km resolution, Arctic Ocean regional simulation ‘How to’ guide |
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Dr Jonny Williams, School of Geographical Sciences, Bristol University, UK |
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jonny.williams@bristol.ac.uk |
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1. cd to your MITgcm central directory and check out the code and (some of the) required |
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input files |
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a. cvs co -d cs_36km_tutorial MITgcm_contrib/arctic/cs_36km/ |
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2. cd to this new directory and make a ‘build’ directory |
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3. Personally I recommend outputting NetCDF files. You will need to do the following if you |
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want to do this |
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a. add a line with “mnc” on it to cs_36km_tutorial/code/packages.conf |
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b. add a line with “useMNC=.TRUE.,” to cs_36km_tutorial/input/data.pkg |
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c. add a “data.mnc” file which you can copy from the input directory of any of the |
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verification experiments that use NetCDF output |
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4. Compile in the usual way (system dependent) |
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NOTE: the ftp sites listed below are no longer available but the files have |
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been moved to: https://ecco.jpl.nasa.gov/drive/files/ECCO2/Arctic/arctic_36km |
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5. The following files are all required in the run directory |
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a. the executable you get when compiling “mitgcmuv” |
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b. ftp://ecco2.jpl.nasa.gov/data2/data/runoff/runoff-360x180x12.bin |
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c. ftp://ecco2.jpl.nasa.gov/data2/data/atmos/jra25/*1979* |
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i. note that the following files may need their “.txt” suffixes removed |
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1. jra25_v10m_1979 |
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2. jra25_u10m_1979 |
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3. jra25_spfh2m_1979 |
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4. jra25_temp2m_1979 |
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d. Also, the run requires the following files which are not included in the |
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ftp://ecco2.jpl.nasa.gov/data2/data/atmos/jra25/ directory (I have simply created |
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cymbolic links to the 1979 equivalents). |
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i. jra25_dlw_1978 |
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ii. jra25_dsw_1978 |
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iii. jra25_rain_1978 |
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e. ftp://ecco2.jpl.nasa.gov/data1/arctic/run_template2/* |
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6. There are some duplicate file names in |
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ftp://ecco2.jpl.nasa.gov/data1/arctic/run_template2/ and cs_36km_tutorial/input and it is |
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crucial that those in the latter are used. I have done this by copying them to my run |
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directory (platform dependent) second to automatically overwrite the other ones. |
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7. The model also requires several files which need to be renamed and so I have created |
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symbolic links to them. |
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a. ln -s OBWv_arctic_210x192.bin OBWv_arctic_210x192_19792014m.bin |
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b. ln -s OBWu_arctic_210x192.bin OBWu_arctic_210x192_19792014m.bin |
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c. ln -s OBWt_arctic_210x192.stable OBWt_arctic_210x192_19792014m.stable |
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d. ln -s OBWt_arctic_210x192.bin OBWt_arctic_210x192_19792014m.bin |
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e. ln -s OBWs_arctic_210x192.stable OBWs_arctic_210x192_19792014m.stable |
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f. ln -s OBWs_arctic_210x192.bin OBWs_arctic_210x192_19792014m.bin |
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g. ln -s OBNv_arctic_210x192.bin OBNv_arctic_210x192_19792014m.bin |
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h. ln -s OBNu_arctic_210x192.bin OBNu_arctic_210x192_19792014m.bin |
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i. ln -s OBNt_arctic_210x192.stable OBNt_arctic_210x192_19792014m.stable |
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j. ln -s OBNt_arctic_210x192.bin OBNt_arctic_210x192_19792014m.bin |
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k. ln -s OBNs_arctic_210x192.stable OBNs_arctic_210x192_19792014m.stable |
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l. ln -s OBNs_arctic_210x192.bin OBNs_arctic_210x192_19792014m.bin |
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m. ln -s OBEv_arctic_210x192.bin OBEv_arctic_210x192_19792014m.bin |
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n. ln -s OBEu_arctic_210x192.bin OBEu_arctic_210x192_19792014m.bin |
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o. ln -s OBEt_arctic_210x192.stable OBEt_arctic_210x192_19792014m.stable |
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p. ln -s OBEt_arctic_210x192.bin OBEt_arctic_210x192_19792014m.bin |
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q. ln -s OBEs_arctic_210x192.stable OBEs_arctic_210x192_19792014m.stable |
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r. ln -s OBEs_arctic_210x192.bin OBEs_arctic_210x192_19792014m.bin |
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8. I suggest changing the following in the “data” file just to get you going |
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a. endtime=86400., |
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i. i.e. 1 day in seconds |
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b. dumpFreq = 2400., |
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i. i.e. outputting data on every timestep, i.e. every 40 minutes in |
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seconds |
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9. Submit the job (platform dependent) |
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10. Note that the NetCDF output from this simulation will consist of one file for each processor |
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(80 by default here, nPx × nPy in the cs_36km_tutorial/code/SIZE.h file). |
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Acknowledgments |
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Getting this simulation to run would not have been possible without Fanny Monteiro in the author’s |
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home institution, members of the MITgcm-support online community and in particular, Dimitris |
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Menemenlis, Renske Gelderloos and Patrick Heimbach. |
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|
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======================= |
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Directory contents for |
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ftp://ecco2.jpl.nasa.gov/data1/arctic/run_template2/ |
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Matlab script "mk_run_template2.m" was used to generate many of the model |
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input files described below. |
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Grid information files needed when OLD_GRID_IO option is defined in |
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CPP_OPTIONS.h. See GRID.h for a digram of various distances. |
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LONC.bin longitude east of cell center |
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LATC.bin latitude north of cell center |
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LONG.bin longitude east of southwest corner of cell |
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LATG.bin latitude north of southwest corner of cell |
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DYF.bin meridional distance in m between V-points |
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DXF.bin zonal distance in m between U-points |
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DYU.bin meridional distance in m between U-points |
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DXV.bin zonal distance in m between V-points |
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DYC.bin meridional distance in m between tracer points |
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DXC.bin zonal distance in m between tracer points |
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DYG.bin meridional distance in m between cell corners |
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DXG.bin zonal distance in m between cell corners |
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RAZ.bin vertical face area in m^2 for vorticity points |
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RAW.bin vertical face area in m^2 for u cells |
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RAS.bin vertical face area in m^2 for v cells |
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RA.bin vertical face area in m^2 for tracer cells |
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Model bathymetry, initial, and surface boundary condition files. |
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ETOPO2_210x192_arctic model bathymetry (m) |
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WGHC_S_210x192x50_arctic initial salinity (g/kg) |
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WGHC_T_210x192x50_arctic initial potential temperature (deg C) |
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AREA_210x192_arctic.cube81 initial ice concentration (fractional >=0, <=1) |
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HEFF_210x192_arctic.cube81 initial effective sea ice thickness (m) |
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HSALT_210x192_arctic.cube81 initial effective sea ice salinity (g/m^2) |
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HSNOW_210x192_arctic.cube81 initial effective snow thickness (m) |
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Open boundary condition files. |
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OBNs_arctic_210x192.stable North open boundary conditions, salinity (g/kg) |
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OBNt_arctic_210x192.stable North open boundary conditions, temperature (deg C) |
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OBNu_arctic_210x192.bin North open boundary conditions, U-velocity (m/s) |
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OBNv_arctic_210x192.bin North open boundary conditions, V-velocity (m/s) |
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OBEs_arctic_210x192.stable South open boundary conditions, salinity (g/kg) |
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OBEt_arctic_210x192.stable South open boundary conditions, temperature (deg C) |
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OBEu_arctic_210x192.bin South open boundary conditions, U-velocity (m/s) |
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OBEv_arctic_210x192.bin South open boundary conditions, V-velocity (m/s) |
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OBWs_arctic_210x192.stable West open boundary conditions, salinity (g/kg) |
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OBWt_arctic_210x192.stable West open boundary conditions, temperature (deg C) |
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OBWu_arctic_210x192.bin West open boundary conditions, U-velocity (m/s) |
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OBWv_arctic_210x192.bin West open boundary conditions, V-velocity (m/s) |
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Runtime parameter files. |
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eedata |
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data |
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data.pkg |
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data.cal |
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data.exf |
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data.gmredi |
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data.seaice |
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data.obcs |
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data.kpp |
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data.salt_plume |
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data.diagnostics |
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